A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-04-01, 12:35 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
nf-core/quantms Software Versions
nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms
| Process Name | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 1.8.1 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| DIANNCFG | sdrf-pipelines | 0.0.21 |
| DIANNCONVERT | sdrf-pipelines | 0.0.21 |
| DIANNSUMMARY | DIA-NN | 1.8.1 |
| DIANN_PRELIMINARY_ANALYSIS | DIA-NN | 1.8.1 |
| INDIVIDUAL_FINAL_ANALYSIS | DIA-NN | 1.8.1 |
| MSSTATS | bioconductor-msstats | 4.2.0 |
| r-base | 4.1.2 | |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms
Core Nextflow options
- runName
- voluminous_thompson
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_dia,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
- outdir
- ./results_dia
Protein database
- database
- /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta
Database search
- allowed_missed_cleavages
- 1
- instrument
- N/A
- max_precursor_charge
- 3
- min_peptide_length
- 15
- max_peptide_length
- 30
- max_mods
- 2
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
- min_pr_mz
- 350
- max_pr_mz
- 950
- min_fr_mz
- 500
- max_fr_mz
- 1500
- diann_normalize
- N/A
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DIA
- config_profile_description
- Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A